9RK3 | pdb_00009rk3

Soluble domain of kustd1480, a Rieske iron-sulfur cluster protein from Kuenenia stuttgartiensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.276 (Depositor), 0.306 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Rieske Iron-Sulfur Cluster Proteins From an Anaerobic Ammonium Oxidizer Suggest Unusual Energetics in Their Parent Rieske/Cytochrome b Complexes.

Hauser, D.Sode, M.Andreeva, E.A.Parey, K.Barends, T.R.M.

(2025) Proteins 

  • DOI: https://doi.org/10.1002/prot.70084
  • Primary Citation of Related Structures:  
    9RK3, 9RK4

  • PubMed Abstract: 

    Anaerobic ammonium-oxidizing (anammox) bacteria employ a unique, hydrazine-based pathway to obtain energy from nitrite and ammonium. These organisms possess distinct Rieske/cytochrome b complexes whose precise role in anammox metabolism remains unclear, but which have been proposed to include the generation of NAD(P)H. This would require energetics and structural features unusual for such complexes. Here we present crystal structures and electrochemical investigations of the Rieske subunits of two of these complexes from the anammox organism Kuenenia stuttgartiensis, Kuste4569 and Kustd1480. Both proteins display high redox potentials (> + 300 mV), which can be in part explained by their crystal structures and which fit perfectly into the energetic scheme of the proposed NAD(P)H generation mechanism. Moreover, AlphaFold3 models of the parent complexes trace out a path for the electrons required for NAD(P)H production, which includes a proposed, novel b-type heme in the membrane-bound part of the complex.


  • Organizational Affiliation
    • Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Similar to Rieske 2Fe-2S iron sulfur protein (Cytochrome b6-F complex)A,
B [auth D]
117Candidatus Kuenenia sp.Mutation(s): 0 
Gene Names: petCKsCSTR_10330KSMBR1_1275kustd1480
EC: 1.10.99.1
UniProt
Find proteins for Q1PYR8 (Kuenenia stuttgartiensis)
Explore Q1PYR8 
Go to UniProtKB:  Q1PYR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1PYR8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.276 (Depositor), 0.306 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.2α = 90
b = 76.15β = 90
c = 79.52γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release